Hi,
Perhaps I'm doing somethign wrong. My application i'm trying
to document has a small starting window, then as you navigate
through it the subsequent windows change size and location though
none are full screen. I want to be able to capture all these
without going 'full screen' to do so.

This is something that I have experienced on a number of
occasions. Here are two things that you could do -

1. Find that largest window size in your application, capture
your screens at that size. Then capture the smaller window placed
on the desktop with solid color. Remember that Captivate always
enables you record / capture additional slides (Edit > Record
Additional Slides...)

2. Capture all the large size windows first, then using a
screen capture tool such as SnagIt take a screen shot of the
smaller window and add this as a graphic to the one existing slides
in your project or on a blank slide with colored background.

*NOTE #1: Notepad may try to reopen. Just close it again and
continue working with your target application. You will have to
move or delete some slides during editing, but this should result
in a movie that includes everything you need.

**NOTE #2: Before beginning this you will need to eliminate
icons and desktop images so the "background" for the smaller
windows is a plain color. Otherwise your users may think they are
having a bad trip following a ingestion of a hallucinogen.